Methods for Detecting Fluorescent Proteins and Animals Having Fluorescent Proteins

ABSTRACT

Provided are methods for detecting expression of nucleic acids encoding mutant fluorescent proteins. In the methods, a nucleic acid encoding a mutant fluorescent protein, or a full complement thereof, is introduced into a cell or organism. The cell or organism is allowed to replicate. Expression of the nucleic acid is detected by emission of fluorescent light. Animals including a nucleic acid encoding a mutant fluorescent protein, or a full complement thereof, are also provided.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a divisional of U.S. patent application Ser. No. 10/314,936, filed Dec. 9, 2002, which is incorporated herein by reference in its entirety.

REFERENCE TO GOVERNMENT GRANT

This invention was made with United States government support awarded by the National Institute of Environmental Health Sciences-MFBSC, Contract # ES05705, NIH-National Institute of Neurological Disorders and Stroke, Contract # NS36998, and National Institute of General Medicine, Contract # GM 57505. The United States has certain rights in this invention.

BIBLIOGRAPHY

Complete bibliographic citations of the references referred to herein by the first author's last name in parentheses can be found in the Bibliography section, immediately preceding the claims.

FIELD OF THE INVENTION

The invention relates to the field of biochemical assays and reagents. More specifically, this invention relates to fluorescent proteins and to methods for their use.

DESCRIPTION OF THE RELATED ART

The number of available fluorescent reporter genes has increased as researchers have isolated genes encoding fluorescent proteins from an increasing variety of organisms and included the genes in cloning cassettes. For example, fluorescent proteins from sea creatures have been used as reporter genes capable of integration into DNA via cloning cassettes. Products of these genes fluoresce under certain wavelengths of light, permitting the tracking of proteins in, e.g., heterologous cells, such as dog and monkey cells. The most commonly used proteins of this nature fluoresce green, and were obtained from the jellyfish, Aequorea victoria, and sea pansy, Renilla reniformis. Additionally, a red fluorescent protein (RFP), known as drFP583, and a turquoise fluorescent protein, known as dsFP483, have been isolated from the IndoPacific mushroom corals (Discosoma sp. “red” and Discosoma striata, respectively). Both Discosoma and Actinodiscus are mushroom corals, soft bodied anthozoans that do not produce an external skeleton. It should be noted that the relationship between the genus Discosoma and the genus Actinodiscus is not well understood. Both Actinodiscus and Discosoma are members of the Actinodiscidae Family, which is a member of the Corallimporpharia (mushroom) Order. The taxonomy of the Corallimporpharia is poorly defined, and therefore, the nature of the relation of Actinodiscus to Discosoma is uncertain. Discosoma and Actinodiscus are believed to be different genera of the same family, but they could be more closely or distantly related.

The availability of a variety of fluorescent proteins and reagents has enhanced the opportunities for researchers employing reporter proteins in their work. Isolated DNAs encoding fluorescent proteins have been mutated to alter their optical properties. For instance, mutating tyrosine at amino acid 66 to histidine in the amino acid composition of the Aequorea green fluorescent protein (GFP) changes this protein to one that fluoresces blue. Changing amino acid 64 from phenylalanine to leucine, amino acid 65 from serine to threonine, and amino acid 145 from tyrosine to phenylalanine generates a GFP that fluoresces at a brighter intensity than the parent molecule and has a shifted excitation optima. In addition, by genetically modifying the amino acid composition of GFP, researchers have been able to change its light absorption/emission characteristics, creating yellow fluorescent proteins.

Fluorescent proteins can be used in a number of assays. In one example, fluorescent proteins can be used in Fluorescence Resonance Energy Transfer (FRET) assays. FRET occurs with fluorophores for which the emission spectrum of one overlaps with the excitation spectrum of the second. When the fluorophores are brought into close proximity, excitation of the “donor” results in emission from the “acceptor.” Pairs of such fluorophores are thus useful for monitoring molecular interactions. Fluorescent proteins, such as GFP, are useful for analysis of protein-protein interactions either in vivo or in vitro if their fluorescent emission and excitation spectra overlap to allow FRET. The donor and acceptor fluorescent proteins may be produced as fusion proteins with the proteins being analyzed for interactions. These types of applications of GFPs are particularly appealing for high throughput assays, because the readout is direct and independent of subcellular localization.

Because of its easily detectable green fluorescence, GFP from Aequorea has been used widely to study gene expression and protein localization. Furthermore, GFP, like other fluorescent proteins, does not require a substrate or cofactor to fluoresce; hence, it is possible to directly express GFP and use it as a reporter in numerous species and in a wide variety of cells. However, factors other than fluorescence color and intensity affect the utility of a protein in research. The stability of many fluorescent proteins makes them undesirable reporters to use if one seeks to determine short term or repetitive events. Moreover, accumulated protein can be toxic to some mammalian cells. For example, certain forms of GFP from Aequorea have been demonstrated to induce apoptosis (Liu, et al.). Although the inventors do not wish to be limited to a single explanation of the toxicity of GFP from Aequorea, it is believed that this is probably due to free radical (H₂O₂) formation which occurs in a 1:1 stoichiometry with GFP production, making high levels of GFP expression particularly toxic. This is believed to be a direct result of chromaphore maturation and is believed to occur in every known GFP.

Photobleaching is another concern with previous fluorescent proteins. Photobleaching is a light induced change in a fluorophore, resulting in the loss of absorption of light of a particular wavelength by the fluorophore. This results in loss of fluorescence of the fluorophore. Many fluorescent proteins rapidly photobleach under excitation. This process is usually reversible but can limit the usefulness of GFP expression, e.g. by reducing time available to photograph specimens. However, where the photobleaching is rapidly reversible, this property makes the fluorescent protein useful for certain applications.

Thus, the need remains for easily expressible fluorescent proteins that have a range of spectral outputs and low toxicity to maximize research capabilities. Such research applications include, but are not limited to, short-lived fluorescent proteins as genetic reporters, which would enable monitoring of short-lived activities. Such research applications further include, but are not limited to, low toxicity fluorescent proteins that would allow long-term monitoring or stable transfection of cells or organisms.

Furthermore, the need also remains for fluorescent proteins having novel emission spectra. This would permit monitoring multiple processes simultaneously and could minimize background fluorescence. It would also increase the choices available for FRET analysis systems. Moreover, fluorescent proteins having brighter relative fluorescence are needed to permit detection of low level expression of the fluorescent proteins.

SUMMARY OF THE INVENTION

The invention, which is defined by the claims set out at the end of this disclosure, is intended to solve at least some of the problems noted above. The invention provides improved fluorescent proteins with enhanced properties e.g., substantially enhanced fluorescence and reduced toxicity. The improved fluorescent proteins are useful in research and can be used, e.g., to determine or detect gene expression, e.g., up- or down-regulation, to monitor promoter activity, to allow longer term monitoring, and to localize proteins.

A new, wild-type red fluorescent protein (RFP) was isolated from an aquatic species believed to be either an Actinodiscus or Discosoma species. This protein is referred to hereinafter as Ac/DsRFP. The invention provides two protein mutants derived from Ac/DsRFP. The mutant RFPs of the invention are referred to herein as Red I and Red II. An isolated nucleic acid encoding each of these and their associated amino acid sequences are also included.

In addition, a novel green fluorescent protein (GFP) was isolated from Montastraea cavernosa. This protein is referred to herein as McGFP. The invention provides two novel proteins derived from McGFP. Preferred novel proteins are referred to herein as Green I and Green II. It was also discovered that certain mutants of McGFP photobleach very quickly.

The invention also provides a nucleic acid construct that includes a first coding sequence that encodes a selected polypeptide and a second coding sequence that encodes a fluorescent protein of the invention. The first coding sequence is fused to the second coding sequence such that expression of the fused sequence yields a fluorescent hybrid protein in which the polypeptide encoded by the first coding sequence is fused to the polypeptide encoded by the second coding sequence.

Vectors including the various isolated nucleic acids of the invention are also provided. Vectors of varying capacities are well known to molecular biologists and can be used to transform a eukaryotic or prokaryotic cell. They can also be used with in vivo and in vitro expression systems.

A method of detecting expression of a nucleic acid encoding a fluorescent protein is also provided. The method includes introducing the nucleic acid of the invention into a cell or organism. In a preferred embodiment, a promoter controls expression of the nucleic acid. Expression of the nucleic acid is detected by emission of fluorescent light, allowing detection of expression of the nucleic acid. In a preferred embodiment, the cell is a eukaryotic cell. In another preferred embodiment, the cell is a prokaryotic cell. The expression of the nucleic acid can be detected in vivo. It can also be detected in vitro and in fixed cells, such as formalin fixed cells.

In a preferred embodiment of the method of detecting expression of a nucleic acid, a gene of interest is fused to nucleic acid encoding a fluorescent protein. The fusion protein may include a subcellular specific locator signal, allowing measurement of expression from the promotor and/or subcellular localization. Expression of the gene of interest is detected by emission of fluorescent light.

Also provided is a cell including a nucleic acid of the invention. In a preferred embodiment, the nucleic acid is integrated into a genome of the cell. In another preferred embodiment, the nucleic acid is not integrated into a genome of the cell. For example, the nucleic acid can exist extrachromosomally.

An animal having an isolated nucleic acid of the invention is additionally provided. In a preferred embodiment, the animal is a zebrafish.

BRIEF DESCRIPTION OF THE DRAWINGS

Preferred exemplary embodiments of the invention are illustrated in the accompanying drawings in which:

FIGS. 1A-1B are a sequence alignment of the DNA encoding two mutant red fluorescent proteins: Red I (SEQ. ID. NO:1) and Red II (SEQ. ID. NO: 3), each of which was generated from a protein originally isolated from Actinodiscus/Discosoma sp. In this and all other alignments, the differences between the sequences being aligned are indicated by a missing monomer in the “consensus” line.

FIG. 2 is an alignment of the amino acids encoded by the DNA sequences of Red I (SEQ. ID. NO: 2) and Red II (SEQ. ID. NO: 4).

FIG. 3 is a graph of a spectral analysis of Red I.

FIG. 4 is a graph of a spectral analysis of Red II.

FIG. 5 is a graph of spectral analyses of Red I and Red II.

FIGS. 6A-6B show a sequence alignment of the DNA encoding two mutant green fluorescent proteins: Green I (SEQ. ID. NO:5) and Green II (SEQ. ID. NO:7), each of which was generated from a protein originally isolated from M. cavernosa.

FIG. 7 is an amino acid alignment of the amino acids encoded by the DNA sequences of Green I (SEQ. ID. NO: 6) and Green II (SEQ. ID. NO:8).

FIG. 8 is a graph of a spectral analysis of Green I.

FIG. 9 is a graph of a spectral analysis of Green II.

FIG. 10 is a graph of spectral analyses of Green I and Green II.

Before explaining embodiments of the invention in detail, it is to be understood that the invention is not limited in its application to the details of construction and the arrangement of the components set forth in the following description or illustrated in the drawings. The invention is capable of other embodiments or being practiced or carried out in various ways. Also, it is to be understood that the phraseology and terminology employed herein is for the purpose of description and should not be regarded as limiting.

DETAILED DESCRIPTION Definitions

For purposes of the present invention, the following definitions apply:

The standard, one-letter codes “A,” “C,” “G,” “T,” and “U” are used herein for the nucleotides adenine, cytosine, guanine, thymine, and uracil, respectively. “N” designates any nucleotide. Oligonucleotide or polynucleotide sequences are written from the 5′-end to the 3′-end.

As used herein, “amino acids” are described in keeping with standard polypeptide nomenclature, J. Biol. Chem., 243:3557-59, (1969). All amino acid residues identified herein are in the natural L-configuration. In keeping with standard polypeptide nomenclature, abbreviations for amino acid residues are as shown in the following Table of Correspondence.

TABLE OF CORRESPONDENCE 1-Letter 3-Letter AMINO ACID Y Tyr L-tyrosine G Gly glycine F Phe L-phenylalanine M Met L-methionine A Ala L-alanine S Ser L-serine I Ile L-isoleucine L Leu L-leucine T Thr L-threonine V Val L-valine P Pro L-proline K Lys L-lysine H His L-histidine Q Gln L-glutamine E Glu L-glutamic acid W Trp L-tryptophan R Arg L-arginine D Asp L-aspartic acid N Asn L-asparagine C Cys L-cysteine

By “protein” and “polypeptide” is meant any chain of amino acids, regardless of length or post-translational modification, e.g., glycosylation or phosphorylation. The synthetic genes of the invention may also encode a variant of a naturally-occurring protein or polypeptide fragment thereof. Preferably, such a protein polypeptide has an amino acid sequence that is at least 85%, preferably 90%, and most preferably 95% or 99% identical to the amino acid sequence of the naturally-occurring (native) protein from which it is derived.

The term “isolated” when used in relation to a nucleic acid, as in “isolated nucleic acid” or “isolated polynucleotide,” refers to a nucleic acid sequence that is identified and separated from at least one contaminant with which it is ordinarily associated in its source. Thus, an isolated nucleic acid is present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated nucleic acids, e.g., DNA and RNA, are found in the state they exist in nature. For example, a given DNA sequence, e.g., a gene, is found on the host cell chromosome in proximity to neighboring genes; RNA sequences, e.g., a specific mRNA sequence encoding a specific protein, are found in the cell as a mixture with numerous other mRNAs that encode a multitude of proteins. However, isolated nucleic acid includes, by way of example, such nucleic acid in cells ordinarily expressing that nucleic acid where the nucleic acid is in a chromosomal location different from that of natural cells, or is otherwise flanked by a different nucleic acid sequence than that found in nature. The isolated nucleic acid may be present in single-stranded or double-stranded form. When an isolated nucleic acid is to be utilized to express a protein, the oligonucleotide contains at a minimum, the sense or coding strand, i.e., the oligonucleotide may be single-stranded, but may contain both the sense and anti-sense strands, i.e., the oligonucleotide may be double-stranded.

The term “isolated” when used in relation to a polypeptide, as in “isolated protein” or “isolated polypeptide” refers to a polypeptide that is identified and separated from at least one contaminant with which it is ordinarily associated in its source. Thus, an isolated polypeptide is present in a form or setting that is different from that in which it is found in nature. In contrast, non-isolated polypeptides, e.g., proteins and enzymes, are found in the state in which they exist in nature.

The term “purified” or “to purify” means the result of any process that removes some of a contaminant from the component of interest, such as a protein or nucleic acid. The percent of a purified component is thereby increased in the sample.

With reference to nucleic acids of the invention, the term “nucleic acid” refers to DNA, genomic DNA, cDNA, RNA, mRNA and a hybrid of the various nucleic acids listed. The nucleic acid can be of synthetic origin or natural origin. A nucleic acid, as used herein, is a covalently linked sequence of nucleotides in which the 3′ position of the pentose of one nucleotide is joined by a phosphodiester group to the 5′ position of the pentose of the next, and in which the nucleotide residues (bases) are linked in specific sequence, i.e., a linear order of nucleotides.

The term “wild-type” as used herein, refers to a gene or gene product that has the characteristics of that gene or gene product isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designated the “wild-type” form of the gene. In contrast, the term “mutant” refers to a gene or gene product that displays modifications in sequence and/or functional properties, i.e., altered characteristics, when compared to the wild-type gene or gene product. It is noted that naturally-occurring mutants can be isolated; these are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.

As used herein, “higher relative fluorescence intensity” or “increased brightness” refers to fluorescence intensity or brightness that is greater than that exhibited by a wild-type fluorescent protein under a given set of conditions. Generally, an increase in fluorescence intensity or brightness means that fluorescence of a variant is at least 25% or more, and preferably greater than 50%, or more, and more preferably greater than 100% or more intense or bright than the wild-type fluorescent protein under a given set of conditions.

The term “nucleic acid construct” denotes a nucleic acid that is composed of two or more nucleic acid sequences that are derived from different sources and that are ligated together using methods known in the art.

The term “host cell” as used herein, refers to a cell from any organism. Preferred host cells are derived from plants, bacteria, yeast, fungi, insects, or other animals. Methods for introducing polynucleotide sequences into various types of host cells are well known in the art. Host cell includes progeny or potential progeny of these designations.

The term “vector” is used in reference to nucleic acid molecules into which fragments of DNA may be inserted or cloned and can be used to transfer DNA segment(s) into a cell and capable of replication in a cell. Vectors may be derived from plasmids, bacteriophages, viruses, cosmids, and the like.

The term “expression vector” as used herein refer to DNA or RNA sequences containing a desired coding sequence and appropriate DNA or RNA sequences necessary for the expression of the operably linked coding sequence in a particular host organism. Prokaryotic expression vectors typically include a promoter, a ribosome binding site, an origin of replication for autonomous replication in a host cell and possibly other sequences, e.g. an optional operator sequence, optional restriction enzyme sites. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and to initiate RNA synthesis. Eukaryotic expression vectors typically include a promoter, optionally a polyadenlyation signal and optionally an enhancer sequence.

The term “operably linked” means that the regulatory sequences necessary for expression of the coding sequence are placed in the DNA molecule in the appropriate positions relative to the coding sequence so as to effect expression of the coding sequence. This same definition is sometimes applied to the arrangement of coding sequences and transcription control elements, e.g., promoters, enhancers, and termination elements, in an expression vector.

In the present invention, there may be employed conventional molecular biology and microbiology within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook, Fritsch & Maniatis, Molecular Cloning: A Laboratory Manual, Third Edition (2001) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

In accordance with the invention, new wild-type fluorescent proteins have been isolated. The wild-type fluorescent proteins have been mutated to create mutant forms of the fluorescent proteins that have, e.g., a higher relative fluorescence intensity or a greater ability to resist photobleaching than their respective wild-type fluorescent proteins.

I. Isolation of Wild-Type Fluorescent Proteins

Briefly, tissue from an organism of interest was collected and homogenized by methods described in detail below. RNA was isolated, and RT-PCR was performed. Size-selected DNA was recovered from an agarose gel, and then ligated into a vector suitable for bacterial selection. The vector can include an inducible or constitutive promoter. In a preferred embodiment, plasmids were used as the vectors. Plasmids were electroporated into competent bacteria. Bacteria were incubated on LB-ampicillin plates (100 μg/ml). Clones of interest were isolated based upon qualitative determination of fluorescence intensity and/or color quality.

Using this procedure, which is explained in detail in the Examples below, a cDNA encoding a wild-type red fluorescent protein was isolated from an aquatic species believed to be Actinodiscus or Discosoma. Because of the uncertainty in the relationship of the genera Actinodiscus or Discosoma, which is discussed above in the Description of the Related Art section, this protein is referred to hereinafter as Ac/DsRFP. The isolated cDNA encoding Ac/DsRFP was further mutated, and isolates were selected based upon properties of interest, as is detailed below. Additionally, using the methods described herein, a cDNA encoding a wild-type green fluorescent protein (GFP) was isolated from Montastraea cavernosa and is referred to herein as McGFP. As is described below, the isolated cDNA encoding McGFP was further mutated, and selected based upon properties of interest.

II. Creation of Mutated Fluorescent Proteins

For each of the wild-type genes isolated, random mutations in the coding sequences were induced in each through PCR conducted under low stringency conditions (low annealing temperature, excessively long extension times, extra cycles, as described below) to induce mutations during the polymerization. The resulting PCR products were cloned into bacterial expression vectors. Clones were screened for increased relative fluorescence, colors of interest, and decreased photobleaching when compared to the corresponding wild-type fluorescent protein. The vector DNA was then purified from selected clones and sequenced to determine the relevant PCR-induced mutational changes. This process was then reiterated several times.

a. Red I and Red II

The DNA encoding the Ac/DsRFP, the wild-type RFP from Discosoma, was mutated as indicated above with several rounds of low stringency PCR. After cloning into a vector and visual screening of transformed bacteria for fluorescent properties, the proteins encoded by Red I and Red II were selected based upon higher relative fluorescence intensity when compared to the parent Ac/DsRFP wild type. Red II has a fluorescent intensity that is at least 50% greater than the intensity of Red I, as determined qualitatively.

The DNA sequences of Red I (SEQ. ID. NO:1) and Red II (SEQ. ID. NO:2) are shown in FIGS. 1A-1B. Compared to the DNA encoding Red I, the DNA encoding Red II contains a single nucleotide difference: at position 694: Red I has a G, and Red II has an A. The amino acid sequences of Red I (SEQ. ID. NO:2) and Red II (SEQ. ID. NO:4) are shown in FIG. 2. This figure indicates that at position 232, Red I has a D, whereas Red II has an N.

Referring now to FIG. 3-5, spectral analyses of Red I and Red II and for both Red I and Red II are shown.

b. Green I and Green II

The DNA sequence encoding, McGFP, the wild-type GFP from M. cavernosa, was mutated using PCR under low stringency conditions, as described herein. A mutant GFP with brighter fluorescence was isolated and is indicated as Green I. A second round of low stringency PCR was performed on Green I, yielding a second mutant GFP with high resistance to photobleaching and is indicated as Green II. When compared to the DNA sequence encoding the Green I, the DNA encoding Green II contains a single nucleotide change: a cytosine to thymine mutation at nucleotide 527, as shown in FIGS. 6A-6B as SEQ.ID.NO:5 and SEQ.ID.NO:7. The amino acid sequences are shown in FIG. 7 as SEQ. ID. NO:6 and SEQ. ID. NO:8. This figure indicates an S at position 176 in Green I, and an F at the same position in Green II.

Green I had higher relative fluorescence intensity when compared to the McGFP. Green II also higher relative fluorescence but also has a high resistance to photobleaching, a property not evident in the Green I protein. Using a mercury arc laser commonly employed in fluorescence microscopy, manipulated by an Attoarc™ HBO 100W variable power supply, Green I was found to photobleach under appropriate conditions. Low laser intensity is considered to be less than 25% intensity, and high laser intensity is considered to be greater than 75% for this instrument. Cells were visualized using a Zeiss Axiovert S100 Microscope. Under low laser intensity, such as 10%, both derivative proteins appear the same. However, after several seconds under high laser intensity, such as 80%, Green I light is not visible. After several minutes in the dark followed by re-illumination, the fluorescence of Green I is again evident. Green I is also unusual in that excitation with 420 nm light rapidly reverses photobleaching. Green II does not undergo this photobleaching response.

Referring to FIGS. 8-10, spectral analyses of Green I (FIG. 8) and Green II (FIG. 9) and for both Green I and Green II (FIG. 10) are shown.

IV. Exemplary Uses of the Fluorescent Proteins

All of the fluorescent proteins described herein can be used as markers to detect expression of a gene of interest such as by inserting the gene of interest and DNA encoding a fluorescent protein into a vector. The vector can be transformed into a eukaryotic or prokaryotic host cells, such as, e.g., bacterial cells, insect cells, yeast cells, and mammalian cells. As is known in the art, host cells are competent or can be rendered competent by a variety of techniques, including, but not limited to, calcium phosphate precipitation, fusion of the recipient cells with bacterial protoplasts containing the DNA, treatment of the recipient cells with liposomes containing the DNA, DEAE dextran, receptor-mediated endocytosis, electroporation, and micro-injection of the DNA directly into the cells. The DNA can be integrated into the chromosomal DNA of the host cell or it can exist extrachromosally, such as via a plasmid.

Fluorescent proteins of the invention can also be used in biochemical assays and as reagents. For example, the fluorescent proteins can be used as a reporter to monitor fermentation processes and to quantify gene expression.

Additionally, the fluorescent proteins of the invention provide additional fluorescent proteins that can be used in multiple labeling systems. For example, one of the GFPs of the invention can be used to label a first population of cells and one of the RFPs of the invention can be used to label a second population of cells such that two different populations of cells can be tracked, e.g., during fluorescence activated cell sorting. Similarly, Red I and Red II can be used, e.g., to label and track different populations of cells because Red I and Red II fluoresce at different wavelengths.

Further, the inventive fluorescent proteins can also be used in prokaryotic and eukaryotic expression systems. For instance, fusion proteins can be generated to contain coding sequences for a fluorescent protein and another gene. A typical fusion protein of the invention includes a first coding sequence that encodes a selected polypeptide and a second coding sequence that encodes a fluorescent protein of the invention. The first coding sequence is fused to the second coding sequence such that expression of the fused sequence yields a fluorescent hybrid protein in which the polypeptide encoded by the first coding sequence is fused to the polypeptide encoded by the second coding sequence. It is believed that the fluorescent proteins of the invention can be fused either at the 3′ or 5′ end of the coding sequence. Furthermore, unlike fusion proteins with coding sequences for proteins such as β-galactosidase, fusion proteins containing coding sequences for a fluorescent protein do not require exogenously added substrates or cofactors. This beneficially permits the fluorescent proteins to be used in living cells.

The fluorescent proteins provided herein can also be used as in vivo markers, such as in mRNA microinjection assays. Other examples of uses of fluorescent proteins are as an in vivo marker in transgenic mice, Caenhorbabditis elegans, Drosophila melanogaster, and Zebrafish.

In addition, fluorescent proteins of the invention can be used as taxonomic markers for studies of cnidarian genetics, color indicators in diagnostic kits, colored food additives, and cosmetic ingredients.

EXAMPLES

The following Examples are provided for illustrative purposes only. The Examples are included herein solely to aid in a more complete understanding of the presently described invention. The Examples do not limit the scope of the invention described or claimed herein in any fashion.

Example 1 Species Collection and Animal Husbandry

Coral colonies were obtained from two sources. First, a solid, brick-red colony consisting of several Actinodiscus/Discosoma sp. polyps was obtained from a local aquarium store. Second, Montastraea cavernosa colonies were collected from reefs in the South Florida area. Both species were maintained in small aquariums with flow-through, filtered sea water.

Example 2 Isolation of Total RNA, Reverse Transcription, Amplification and Recovery of cDNAs

RNA was isolated using the Totally RNA kit (Catalog #1902, Ambion, Inc., Austin, Tex.) from a single polyp (Actinodiscus/Discosoma sp.) or from a cellular mass lightly airbrushed from the underlying skeleton (M. cavernosa). Briefly, the tissue was homogenized and mixed by tube inversion with approximately 10 volumes of denaturation solution and extracted with 1 volume of phenol/chloroform. The aqueous supernatant was transferred to a clean vessel. One-tenth volume of 3M sodium acetate was added to the supernatant, which was then extracted an additional time with 1 volume of acid-phenol/chloroform. Again, the aqueous supernatant was transferred to a clean vessel. One volume of isopropanol was added to the supernatant, and total RNA was precipitated by centrifugation. The pellet was washed with 75% ethanol and resuspended in 50 uL RNAse-free water. Yield was measured with a spectrophotometer, and quality was assessed by gel electrophoresis.

The RNA thus isolated was used in a First Choice™ RLM-RACE kit (catalog #1700, Ambion, Inc.) to create and amplify cDNAs. The “small reaction” protocol, as per RLM-RACE protocol version 0010, was followed. Briefly, total RNA is treated with Calf intestinal phosphatase (CIP) to remove 5′ phosphates from degraded and non-capped RNA, and then phenol:chloroform extracted. Tobacco acid pyrophosphatase (TAP) was then used to remove the cap from full-length mRNA. An included 5′ RACE adaptor (5′-GCUGAUGGCGAUGAAUGAACACUGCGUUUGCUGGCUUUGAUGAAA-3′) (SEQ. ID. NO:9) was ligated to total decapped mRNAs with T4 RNA ligase. Reverse transcription was accomplished using MMLV reverse transcriptase and a polyT primer (5′-CTCGAGAAGCTTGAATTCGGATCCTTTTTTTTTTTTTTTTT-3′) (SEQ. ID. NO:10).

Amplification of the resultant cDNA was done using the same polyT primer, the 5′ RACE Outer Primer (5′-GCTGATGGCGATGAATGAACACTG-3′) (SEQ. ID. NO:11) and SuperTaq Polymerase (Ambion, Inc., catalog 2050).

PCR was conducted as follows: 94° C./5 min, 80° C. hold, add polymerase, 34 cycles of 94° C./30 sec, 60° C./1 min, 72° C./1 min and a final 10 min of 72° C. Amplified cDNAs were gel purified. The fraction from about 500-1200 base pair (bp) was collected and recovered by slow speed centrifugation through siliconized glass wool followed by isopropanol precipitation.

Example 3 Transformation and Selection of Bacterial clones, Plasmid Preparation, and DNA Sequencing of Wild-Type Fluorescent Proteins

The gel purified cDNA fraction was ligated into the pCR II cloning vector (Invitrogen, Carlsbad, Calif.), with resultant plasmids electrotransformed into Top 10 E. coli (Invitrogen). Transformed bacteria were grown on LB-ampicillin (100 μg/ml) plates and colonies were screened for fluorescence using a Leica MZFLIII fluorescence stereo dissection microscope. Single fluorescent colonies were picked, restreaked for several rounds to resolve mosaicism, and grown in liquid culture. Plasmid DNA was prepared using the Qiagen Midi kit (Qiagen, Valencia, Calif.).

A colony expressing a wild-type red fluorescent protein (RFP) was isolated from the bacterial colonies generated from the Actinodiscus/Discosoma sp. 1 RNA. This is herein referred to as Ac/DsRFP.

In addition, a colony expressing a wild-type green fluorescent protein (GFP) was isolated from the bacterial colonies generated from the M. cavernosa RNA and was named McGFP.

Example 4 Generation of Mutations of Fluorescent Proteins

Each of the genes coding for the wild-type proteins was subject to error-prone PCR. The PCR products were cloned, and were selected qualitatively based on expression of proteins encoded by the PCR products.

Specifically, a 5′ “upper” primer containing a Kpn I restriction site, Shine-Dalgamo and Kozak consensus uptranslation sequences, the starting ATG of the coding region, and approximately 10 bp of downstream homology was designed for both Ac/DsRFP and McGFP. The upper primer for Ac/DsRFP was:

(SEQ. ID. NO:12) 5′-CCGGTACCTAAGGAGGCCACCATGAGTTGTTCC-3′ and the upper primer for McGFP was:

(SEQ. ID. NO:13) 5′-CCGGTACCTAAGGAGGCCACCATGAGTGTGATAAAAC-3′.

A 3′ “lower” primer containing an Xba I restriction site, the stop codon of the coding region, and approximately 10 bp of upstream homology was also designed for each of the fluorescent protein isolates. The lower primer for Ac/DsRFP was:

(SEQ. ID. NO:14) 5′-CCACTAGTCTAGATCATTACCGCTC-3′ and the lower primer for McGFP was:

(SEQ. ID. NO:15) 5′-GGTCTAGATTACTTGGCCTGCCTC-3′.

Low-stringency PCR protocol was performed on the fluorescent protein plasmid DNA using the above primers. The conditions were: 94° C./5 min, 80° C./hold, add polymerase, 10 cycles of 94° C./1 min, 42° C./2 min, 72° C./3 min, 30 cycles of 94° C./30 sec, 55° C./1 min, 72° C./1 min and a final 10 min of 72° C. The PCR products were purified with a phenol/chloroform extraction and isopropanol precipitation, digested with Kpn I/Xba I, gel purified, and ligated into Kpn I/Xba I digested pBS II KS+ plasmid (Stratagene, La Jolla, Calif.). The ligation mix was electrotransformed into Top 10 cells (Invitrogen) and colonies were screened for 1) brightness greater than parent, 2) speed of color development, 3) size, and 4) color.

Two mutants were generated from Ac/DsRFP, the wild-type red fluorescent protein by several rounds of low stringency PCR, as described above. After cloning into a vector and visual screening of transformed bacteria for fluorescent properties, the proteins encoded by Red I and Red II were selected based upon higher relative fluorescence intensity when compared to the parent Ac/DsRFP wild type. The mutant clones generated were named Red I and Red II.

In addition, the Green I mutant was generated from the McGFP, the wild-type green fluorescent protein. A second round of low-stringency PCR was performed on the DNA encoding Green I, and colonies meeting the above four criteria were isolated. The mutant clone generated from Green I was named Green II. Sequencing was performed by The University of Iowa DNA Facility (Iowa City, Iowa) using purified plasmid preparations. The DNA sequences of Red I and Red II are shown in FIGS. 1A-1B, and the amino acid sequences are shown in FIG. 2. The DNA sequences of Green I and Green II are shown in FIGS. 6A-6B, and the amino acid sequences are shown in FIG. 7.

Example 5 Fluorescent Proteins Cloned into Other Expression Vectors and Spectral Analysis Thereof

For mammalian expression, each of the four mutant fluorescent proteins (Red I, Red II, Green I, and Green II) was restriction digested with KpnI/XbaI, then T4 DNA polymerase treated to create blunt ends, and cloned into pCI-neo Mammalian Expression Vector (Promega, Madison, Wis.) using the blunt end SmaI restriction site to generate pCI-Neo-Red I, pCI-Neo-Red II, pCI-Neo-Green I, and pCI-Neo-Green II.

Spectral analysis was determined on the fluorescent proteins expressed in both mammalian and bacterial cells. Mammalian CHO cells were transfected with pCI-Neo-Red I, pCI-Neo-Red II, pCI-Neo-Green I, or pCI-Neo-Green II plasmid using Trans-Fast™ Transfection Product (Promega). Spectral analysis was determined on cell lysis of the transfected CHO cells using a Spex Fluorolog 1680 0.22 m Double Spectrometer. Red II and Green II plasmids were also expressed in prokaryotic cells. The fragment of the appropriate plasmids was PCR amplified with oligonucleotides that generate NcoI-NotI restriction sites. The PCR amplicons were digested with NcoI and NotI and cloned into the same sites in a prokaryotic expression vector, which was then used to transform E. coli JM109 bacteria. After purification of fluorescent proteins, excitation and emission spectra for some proteins were collected and other proteins were evaluated visually using the Zeiss microscope. Note that the spectra were recorded at 24 hours, however, mature fluorescence for Red II takes more than 24 hours, and by 48 hours, the emission peak is at 583 nm.

Example 6 Transgenic Animals Expressing the Fluorescent Protein

DNA for microinjection into zebrafish embryos was prepared as described previously (Gibbs et al., 1994), with a final concentration of approximately 2 μg/ml linear DNA and 0.05% phenol red. Under a dissecting microscope, several hundred newly fertilized eggs in embryo rearing solution (ERS—tap water with 25 mg/L neomycin sulfate, 0.5 mg/L methylene blue, 17.5 mg/L sodium thiosulfate, and 125 ul/L Amquel [Kordon]) were placed in a 35 mm petri dish of 1% agar containing a single depression of 1-2 mm. With the left hand, a single egg with an intact chorion was rolled into the depression using a number 5 forceps and held in place with the animal pole upright. With the right hand, the egg was microinjected with a running syringe (Gilmont S-1100 with a 5-10 micron needle tip) into the central lower region of the first cell near the yolk-cytoplasm boundary. Disruption of this boundary and leakage of the DNA solution into the underlying yolk occurred in most eggs and did not harm the resultant embryos. After microinjection, the egg was moved with the left-hand forceps to a 100 mm petri dish containing ERS, and the next egg was rolled into position in the depression. Using this technique 500 or more eggs could be microinjected a day. The average dose per embryo, as established by Southern blot analysis, was 50 pg of DNA. This dose was empirically chosen because it resulted in a high proportion of gene transfer. Under these conditions, approximately half of the embryos died in the first 24 hours, and survival to sexual maturity was expected from 10% to 20% of the eggs injected. However, survival of embryos that were mock injected (received no DNA) was approximately 90% that of controls receiving no treatment.

Living embryos and whole mount tissues from fish were observed and photographed with a Leica MZFL III stereo fluorescence dissection microscope equipped with a camera. The filter sets used were an FITC filter set (excitation, 470 nm; emission 515 nm), a modified FITC filter set (Leica-GFP) (excitation, 425 nm; emission, 480 nm) or a rhodamine filter set (excitation, 546 nm; emission, 590 nm). Embryos were individually transferred by pipette in an approximately 50 μl drop of ERS to an inverted 100 mm petri dish lid and observed in groups of about 50 embryos. To immobilize embryos for photography or detailed observation, 1 ml of a 20× stock anesthetic was added to the approximate 20 ml of ERS in a 100 mm petri dish. The 20× stock anesthetic was 3 g/L of tricaine methanesulfonate (MS-222), 20 mM Tris, pH 8, in ERS. Anesthetized embryos, with or without an intact chorion, became immobile in about 2 minutes and remained viable in this solution for at least 30 minutes. After observation, the embryos were moved to a fresh dish of ERS and regained their mobility in several minutes.

Embryos microinjected with linearized fish expression DNA vectors at the one-cell stage containing either Red II or Green II could be scored as positive for expression of fluorescent proteins within 24 hours. Typically, greater than 50% of the embryos contained fluorescent cells or patches which were retained in about 10% of the individuals upon maturity. From one of the adult fish containing a fluorescent patch of Red II expression, a line of fish has been derived in which Red II is ubiquitously expressed from the embryo through the adult.

BIBLIOGRAPHY

-   Fradkov, A. F., et al. (2000) Novel Fluorescent protein from     Discosoma coral and its mutants possesses a unique far-red     fluorescence. FEBS Letters 479:127-130. -   Gibbs, P. D. L., Peek, A., and Thorgaard, G. (1994) An in vivo     screen for the luciferase transgene in zebrafish. Mol. Mar. Biol.     Biotechnol. 3:307-316. -   Gibbs, P. D. L. & Schmale, M. C. (March/April 2000) GFP as a Genetic     Marker Scorable Throughout the Life Cycle of Transgenic Zebrafish.     Marine Biotechnology. 2:107-125. -   Liu, H. S., et al. (1999) Is Green Fluorescent Protein Toxic to the     Living Cells? Biochemical & Biophysical Research Communications     260:712-717. -   Matz, M. V., et al. (October 1999) Fluorescent proteins from     nonbioluminescent Anthozoa species. Nature Biotech 17:969-973. -   Ormo, M., et al. (1996) Crystal structure of the Aequorea victoria     green fluorescent protein. Science 273:1392-1395. -   Yang, F., Moss, L. G., and Phillips, G. N., Jr. (1996) The Molecular     Structure of GFP. Nature Biotech 14:1246-1251.

All publications, patents and patent applications are incorporated herein by reference. While in the foregoing specification, this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details herein may be varied considerably without departing from the basic principles of the invention. 

1. A method comprising: introducing a nucleic acid encoding a mutant red fluorescent protein, or a full complement thereof, into a cell or organism; allowing the cell or organism to replicate; and detecting expression of the nucleic acid by emission of fluorescent light.
 2. The method of claim 1, wherein the nucleic acid is introduced into a eukaryotic cell.
 3. The method of claim 1, wherein the nucleic acid is introduced into a prokaryotic cell.
 4. The method of claim 1, wherein the expression of the nucleic acid expression is detected in vivo.
 5. The method of claim 1, wherein the expression of the nucleic acid is detected in vitro.
 6. The method of claim 1, wherein the nucleic acid comprises SEQ ID NO: 1 (Red I) or a full cDNA of SEQ ID NO:
 1. 7. The method of claim 1, wherein the nucleic acid comprises SEQ ID NO: 3 (Red II) or a full cDNA of SEQ ID NO:
 3. 8. An animal comprising a nucleic acid encoding a mutant red fluorescent protein, or a full complement thereof.
 9. The animal of claim 8, wherein the animal is a zebrafish.
 10. The animal of claim 8, wherein the nucleic acid comprises SEQ ID NO: 1 (Red I) or a full cDNA of SEQ ID NO:1.
 11. The animal of claim 8, wherein the nucleic acid comprises SEQ ID NO: 3 (Red II) or a full cDNA of SEQ ID NO:
 3. 12. A method comprising introducing a nucleic acid encoding a mutant green fluorescent protein, or a full complement thereof, into a cell or organism; allowing the cell or organism to replicate; and detecting expression of the nucleic acid by emission of fluorescent light.
 13. The method of claim 12, wherein the nucleic acid is introduced into a eukaryotic cell.
 14. The method of claim 12, wherein the nucleic acid is introduced into a prokaryotic cell.
 15. The method of claim 12, wherein the expression of the nucleic acid is detected in vivo.
 16. The method of claim 12, wherein the expression of the nucleic acid is detected in vitro.
 17. The method of claim 12, wherein the nucleic acid comprises SEQ ID NO: 5 (Green I) or a full cDNA of SEQ ID NO:5.
 18. The method of claim 12, wherein the nucleic acid comprises SEQ ID NO: 7 (Green II) or a full cDNA of SEQ ID NO:7.
 19. An animal comprising a nucleic acid encoding a mutant green fluorescent protein, or a full complement thereof.
 20. The animal of claim 19, wherein the animal is a zebrafish.
 21. The method of claim 19, wherein the nucleic acid comprises SEQ ID NO: 5 (Green I) or a full cDNA of SEQ ID NO:5.
 22. The animal of claim 19, wherein the nucleic acid comprises SEQ ID NO: 7 (Green II) or a full cDNA of SEQ ID NO:7.
 23. A transgenic cell comprising an isolated nucleic acid comprising SEQ ID NO: 1 (Red I) or a full cDNA of SEQ ID NO:1.
 24. The cell of claim 23, wherein the nucleic acid is integrated into a genome of the cell.
 25. The cell of claim 23, wherein the nucleic acid is not integrated into a genome of the cell.
 26. A transgenic cell comprising an isolated nucleic acid comprising SEQ ID NO: 5 (Green I) or a full cDNA of SEQ ID NO:
 5. 27. The cell of claim 26, wherein the nucleic acid is integrated into a genome of the cell.
 28. The cell of claim 26, wherein the nucleic acid is not integrated into a genome of the cell.
 29. A transgenic cell comprising an isolated nucleic acid comprising SEQ ID NO: 3 (Red II) or a full cDNA of SEQ ID NO:
 3. 30. The cell of claim 29, wherein the nucleic acid is integrated into a genome of the cell.
 31. The cell of claim 29, wherein the nucleic acid is not integrated into a genome of the cell.
 32. A transgenic cell comprising An isolated nucleic acid comprising SEQ ID NO: 7 (Green II) or a full cDNA of SEQ ID NO:
 7. 33. The cell of claim 32, wherein the nucleic acid is integrated into a genome of the cell.
 34. The cell of claim 32, wherein the nucleic acid is not integrated into a genome of the cell. 